We present a temporal and spectral analysis of the gamma-ray flux from nine of the brightest flat spectrum radio quasars (FSRQs) detected with the Fermi Large Area Telescope (LAT) during its first eight years of operation, with the aim of constraining the location of the emission region. Using the increased photon statistics provided from the two brightest flares of each source, we find evidence of sub-hour variability from B2 1520+31, PKS 1502+106 and PKS 1424-41, with the remaining sources showing variability on timescales of a few hours. These indicate gamma-ray emission from extremely compact regions in the jet, potentially compatible with emission from within the broad line region (BLR). The flare spectra show evidence of a spectral cut-off in 7 of the 18 flares studied, further supporting the argument for BLR emission in these sources. An investigation into the energy dependence of cooling timescales finds evidence for both BLR origin and emission from within the molecular torus (MT). However, Monte Carlo simulations show that the very high energy (VHE) emission from all sources except 3C 279, 3C 454.3 and 4C 21.35 is incompatible with a BLR origin. The combined findings of all the approaches used suggest that the gamma-ray emission in the brightest FSRQs originates in multiple compact emission regions throughout the jet, within both the BLR and the MT.
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